├── .bowerrc ├── .gitignore ├── .gitmodules ├── .perltidyrc ├── AUTHORS ├── LICENSE ├── README.md ├── api.sh ├── bin ├── JalView │ └── jalviewApplet.jar ├── NJPlot │ └── njplot-2.3 │ │ ├── README │ │ ├── bigtree.phb │ │ ├── example.phb │ │ ├── helpers.html │ │ ├── makefile │ │ ├── multi.phb │ │ ├── njplot-vib.c │ │ ├── njplot.1 │ │ ├── njplot.gif │ │ ├── njplot.help │ │ ├── njplot.html │ │ ├── preptree.c │ │ ├── unrooted-vib.c │ │ └── unrooted.1 ├── Tabix │ ├── Tabix.pm │ └── TabixIterator.pm ├── aragorn1.2 ├── blastz_wrapper │ └── blastz.py ├── codeml │ ├── codeml-coge │ ├── codeml.ctl │ └── src │ │ ├── Makefile │ │ ├── Makefile.MSVC │ │ ├── Makefile.UNIX │ │ ├── README.txt │ │ ├── TreeTimeJeff.c │ │ ├── baseml │ │ ├── baseml.c │ │ ├── basemlg │ │ ├── basemlg.c │ │ ├── chi2 │ │ ├── chi2.c │ │ ├── codeml │ │ ├── codeml.c │ │ ├── ds.c │ │ ├── evolver │ │ ├── evolver.c │ │ ├── mcmctree │ │ ├── mcmctree.c │ │ ├── out.txt │ │ ├── paml.h │ │ ├── pamp │ │ ├── pamp.c │ │ ├── rst │ │ ├── rst1 │ │ ├── rub │ │ ├── tools.c │ │ ├── treespace.c │ │ ├── treesub.c │ │ ├── yn00 │ │ └── yn00.c ├── convert_long_blast_to_short_blast_names.pl ├── dagchainer │ ├── DAGCHAINER │ │ ├── Java_XY_plotter │ │ │ ├── lib │ │ │ │ ├── DatabaseMatch.class │ │ │ │ ├── DatabaseMatch.java │ │ │ │ ├── EvalueSlider$1.class │ │ │ │ ├── EvalueSlider.class │ │ │ │ ├── EvalueSlider.java │ │ │ │ ├── JsyntenyView$1.class │ │ │ │ ├── JsyntenyView$StringPair.class │ │ │ │ ├── JsyntenyView.class │ │ │ │ ├── JsyntenyView.java │ │ │ │ ├── MatchDiagonal.class │ │ │ │ ├── MatchDiagonal.java │ │ │ │ ├── RangeTree │ │ │ │ │ ├── RTleaf.class │ │ │ │ │ ├── RTleaf.java │ │ │ │ │ ├── RTpoint.class │ │ │ │ │ ├── RTpoint.java │ │ │ │ │ ├── RangeTree.class │ │ │ │ │ └── RangeTree.java │ │ │ │ ├── SequenceFeature.class │ │ │ │ ├── SequenceFeature.java │ │ │ │ ├── SequenceTicker.class │ │ │ │ ├── SequenceTicker.java │ │ │ │ ├── XYplot$1.class │ │ │ │ ├── XYplot$2.class │ │ │ │ ├── XYplot$3.class │ │ │ │ ├── XYplot$4.class │ │ │ │ ├── XYplot$5.class │ │ │ │ ├── XYplot$6.class │ │ │ │ ├── XYplot$XYcanvas.class │ │ │ │ ├── XYplot.class │ │ │ │ └── XYplot.java │ │ │ └── run_XYplot.pl │ │ ├── Makefile │ │ ├── NOTES_BY_COGE │ │ ├── README │ │ ├── accessory_scripts │ │ │ ├── chain_to_length_ratio.pl │ │ │ ├── count_genes_min_chain_len.pl │ │ │ ├── dagchainer_to_chain_spans.pl │ │ │ ├── dagchainer_to_gnuplot.pl │ │ │ ├── extract_only_chromo_pairs_with_dups.pl │ │ │ ├── filter_repetitive_matches.pl │ │ │ ├── findTandemGeneDuplicates.pl │ │ │ ├── limit_to_top_N_hits.pl │ │ │ ├── min_chain_len_filter.pl │ │ │ ├── report_dist_between_chain_segments.pl │ │ │ ├── separateDataSets.pl │ │ │ └── sum_genome_chain_nr_content.pl │ │ ├── dagchainer. │ │ ├── dagchainer.LINUX │ │ ├── dagchainer.cpp │ │ ├── dagchainer.x86_64-linux │ │ ├── docs │ │ │ ├── arab_xyplot.gif │ │ │ ├── arab_xyplot.half.gif │ │ │ ├── dagchainer_150dpi.jpg │ │ │ ├── dagchainer_documentation.asciidoc │ │ │ ├── dagchainer_documentation.html │ │ │ ├── tryp_xy.gif │ │ │ ├── tryp_xy.small.gif │ │ │ ├── xy_plotter_images │ │ │ │ ├── arab_2vs4.gif │ │ │ │ ├── arab_2vs4.select.gif │ │ │ │ ├── arab_2vs4.select.small.gif │ │ │ │ ├── arab_2vs4.small.gif │ │ │ │ ├── arab_2vs4.with_chains.gif │ │ │ │ ├── arab_2vs4.with_chains.small.gif │ │ │ │ ├── arab_2vs4.zoomed.e-value.menu.gif │ │ │ │ ├── arab_2vs4.zoomed.e-value.menu.small.gif │ │ │ │ ├── arab_2vs4.zoomed.gene_selection.gif │ │ │ │ ├── arab_2vs4.zoomed.gene_selection.small.gif │ │ │ │ ├── arab_2vs4.zoomed.gif │ │ │ │ ├── arab_2vs4.zoomed.small.gif │ │ │ │ ├── arab_2vs4.zoomed.unique_matches.gif │ │ │ │ └── arab_2vs4.zoomed.unique_matches.small.gif │ │ │ ├── xy_plotter_tutorial.asciidoc │ │ │ └── xy_plotter_tutorial.html │ │ ├── logo │ │ │ ├── dagchainer_150dpi.jpg │ │ │ ├── dagchainer_300dpi.jpg │ │ │ └── dagchainer_600dpi.jpg │ │ └── run_DAG_chainer.pl │ ├── dag_tools.py │ ├── filter_repetitive_matches.pl │ ├── find_nearby.py │ └── tandems.py ├── dagchainer_bp │ ├── Makefile │ ├── README.rst │ ├── cdagline.so │ ├── dag_chainer.py │ ├── dagchainer │ ├── dagchainer.cpp │ ├── dagtools.egg-info │ │ ├── PKG-INFO │ │ ├── SOURCES.txt │ │ ├── dependency_links.txt │ │ ├── entry_points.txt │ │ ├── not-zip-safe │ │ └── top_level.txt │ ├── dagtools │ │ ├── __init__.py │ │ ├── cdagline.c │ │ ├── cdagline.pyx │ │ ├── evalue_adjust.py │ │ ├── find_nearby.py │ │ ├── from_blast.py │ │ └── plot_dag.py │ ├── dist │ │ └── dagtools-0.1-py2.6-linux-x86_64.egg │ └── setup.py ├── dataset_group_2_bed.pl ├── dialign2_dir │ ├── BLOSUM │ ├── dialign2-2_coge │ ├── tp400_dna │ ├── tp400_prot │ └── tp400_trans ├── dotplot.pl ├── gcat │ ├── Cargo.toml │ └── src │ │ └── main.rs ├── histogram.pl ├── ks_histogram.pl ├── lagan-64bit │ ├── 1512.anchs.final │ ├── ERICLYONS_NOTES.txt │ ├── Makefile │ ├── Readmes │ │ ├── LICENSE │ │ ├── README.FIRST │ │ ├── README.chaos │ │ ├── README.lagan │ │ ├── README.mlagan │ │ ├── README.shuffle │ │ └── README.tools │ ├── Utils.pm │ ├── anal_gloc.pl │ ├── anchors │ ├── blosum62.txt │ ├── blosum62s.txt │ ├── chaos │ ├── chaos_coge │ ├── glocal │ ├── lagan.pl │ ├── lagan.pl.orig │ ├── mlagan │ ├── nucmatrix.txt │ ├── old │ │ └── prolagan │ ├── order │ ├── prolagan │ ├── rechaos.pl │ ├── rechaos.pl.orig │ ├── sample.fasta │ ├── sample.params │ ├── slagan-mfa.pl │ ├── slagan.pl │ ├── src │ │ ├── Makefile │ │ ├── Utils.pm │ │ ├── anal_gloc.pl │ │ ├── anchors.c │ │ ├── ancseq.cpp │ │ ├── ancseqrest.cpp │ │ ├── cutmfa.cpp │ │ ├── diagmatrix.c │ │ ├── diagmatrix.h │ │ ├── faindex.cpp │ │ ├── fchaos.c │ │ ├── fchaos.h │ │ ├── filebuffer.c │ │ ├── filebuffer.h │ │ ├── global.c │ │ ├── global.h │ │ ├── glocal │ │ │ ├── Makefile │ │ │ ├── default.score │ │ │ ├── glocal │ │ │ ├── glocal.cpp │ │ │ ├── glocal.h │ │ │ ├── io.cpp │ │ │ ├── io.h │ │ │ ├── leftinfluence.cpp │ │ │ ├── leftinfluence.h │ │ │ ├── rightinfluence.cpp │ │ │ ├── rightinfluence.h │ │ │ ├── score.cpp │ │ │ ├── score.h │ │ │ ├── structs.h │ │ │ └── test.score │ │ ├── lagan.pl │ │ ├── lagan2mfa.cpp │ │ ├── makecons.cpp │ │ ├── mempage.c │ │ ├── mempage.h │ │ ├── mlagan.c │ │ ├── multial.c │ │ ├── multial.h │ │ ├── order.c │ │ ├── order.h │ │ ├── prolagan.c │ │ ├── rechaos.pl │ │ ├── skiplist.c │ │ ├── skiplist.h │ │ ├── slagan-mfa.pl │ │ ├── slagan.pl │ │ ├── sortlist.c │ │ ├── supermap.pl │ │ ├── thrtrie.c │ │ ├── thrtrie.h │ │ ├── translate.c │ │ ├── translate.h │ │ ├── util.cpp │ │ ├── utils │ │ │ ├── Glue.cpp │ │ │ ├── MultiSequence.h │ │ │ ├── Output.h │ │ │ ├── SafeVector.h │ │ │ ├── Sequence.h │ │ │ ├── bin2bl.c │ │ │ ├── bin2mf.c │ │ │ ├── cextract.c │ │ │ ├── cmerge2.pl │ │ │ ├── contigorder.c │ │ │ ├── cstat.c │ │ │ ├── dotplot.cpp │ │ │ ├── draft.pl │ │ │ ├── fa2xfa.c │ │ │ ├── getbounds.c │ │ │ ├── getcontigpos.c │ │ │ ├── getlength.c │ │ │ ├── getoverlap.c │ │ │ ├── mextract.pl │ │ │ ├── mf2bin.pl │ │ │ ├── mpretty.pl │ │ │ ├── mproject.pl │ │ │ ├── mrun.pl │ │ │ ├── mrunfile.pl │ │ │ ├── mrunpairs.pl │ │ │ ├── mviz.pl │ │ │ ├── overlay.c │ │ │ ├── rc.c │ │ │ ├── scorealign.c │ │ │ ├── scorecontigs.c │ │ │ └── seqmerge.c │ │ └── xmfa2mfa.pl │ ├── supermap.pl │ ├── test.score │ ├── utils │ │ ├── Glue │ │ ├── Utils.pm │ │ ├── bin2bl │ │ ├── bin2mf │ │ ├── cextract │ │ ├── cmerge2.pl │ │ ├── contigorder │ │ ├── cstat │ │ ├── dotplot │ │ ├── draft.pl │ │ ├── fa2xfa │ │ ├── flipchaos.pl │ │ ├── getbounds │ │ ├── getcontigpos │ │ ├── getlength │ │ ├── getoverlap │ │ ├── mextract.pl │ │ ├── mf2bin.pl │ │ ├── mpretty.pl │ │ ├── mproject.pl │ │ ├── mrun.pl │ │ ├── mrunfile.pl │ │ ├── mrunpairs.pl │ │ ├── msplit.pl │ │ ├── mviz.pl │ │ ├── overlay │ │ ├── rc │ │ ├── scorealign │ │ ├── scorecontigs │ │ └── seqmerge │ └── xmfa2mfa.pl ├── last_wrapper │ ├── Bio │ │ ├── Affy │ │ │ ├── CelFile.py │ │ │ └── __init__.py │ │ ├── Align │ │ │ ├── AlignInfo.py │ │ │ ├── Applications │ │ │ │ ├── _Clustalw.py │ │ │ │ ├── _Dialign.py │ │ │ │ ├── _Mafft.py │ │ │ │ ├── _Muscle.py │ │ │ │ ├── _Prank.py │ │ │ │ ├── _Probcons.py │ │ │ │ ├── _TCoffee.py │ │ │ │ └── __init__.py │ │ │ ├── Generic.py │ │ │ └── __init__.py │ │ ├── AlignIO │ │ │ ├── ClustalIO.py │ │ │ ├── EmbossIO.py │ │ │ ├── FastaIO.py │ │ │ ├── Interfaces.py │ │ │ ├── NexusIO.py │ │ │ ├── PhylipIO.py │ │ │ ├── StockholmIO.py │ │ │ └── __init__.py │ │ ├── Alphabet │ │ │ ├── IUPAC.py │ │ │ ├── Reduced.py │ │ │ └── __init__.py │ │ ├── Application │ │ │ └── __init__.py │ │ ├── Blast │ │ │ ├── Applications.py │ │ │ ├── NCBIStandalone.py │ │ │ ├── NCBIWWW.py │ │ │ ├── NCBIXML.py │ │ │ ├── ParseBlastTable.py │ │ │ ├── Record.py │ │ │ └── __init__.py │ │ ├── CAPS │ │ │ └── __init__.py │ │ ├── Cluster │ │ │ ├── __init__.py │ │ │ └── cluster.py │ │ ├── Compass │ │ │ └── __init__.py │ │ ├── Crystal │ │ │ └── __init__.py │ │ ├── Data │ │ │ ├── CodonTable.py │ │ │ ├── IUPACData.py │ │ │ └── __init__.py │ │ ├── DocSQL.py │ │ ├── Emboss │ │ │ ├── Applications.py │ │ │ ├── Primer3.py │ │ │ ├── PrimerSearch.py │ │ │ └── __init__.py │ │ ├── Entrez │ │ │ ├── DTDs │ │ │ │ ├── EMBL_General.mod.dtd │ │ │ │ ├── GenBank_General.mod.dtd │ │ │ │ ├── HomoloGene.dtd │ │ │ │ ├── HomoloGene.mod.dtd │ │ │ │ ├── NCBI_Biblio.mod.dtd │ │ │ │ ├── NCBI_BioSource.mod.dtd │ │ │ │ ├── NCBI_BlastOutput.dtd │ │ │ │ ├── NCBI_BlastOutput.mod.dtd │ │ │ │ ├── NCBI_Entity.mod.dtd │ │ │ │ ├── NCBI_Entrezgene.dtd │ │ │ │ ├── NCBI_Entrezgene.mod.dtd │ │ │ │ ├── NCBI_GBSeq.dtd │ │ │ │ ├── NCBI_GBSeq.mod.dtd │ │ │ │ ├── NCBI_Gene.mod.dtd │ │ │ │ ├── NCBI_General.mod.dtd │ │ │ │ ├── NCBI_Medline.mod.dtd │ │ │ │ ├── NCBI_Mim.dtd │ │ │ │ ├── NCBI_Mim.mod.dtd │ │ │ │ ├── NCBI_Organism.mod.dtd │ │ │ │ ├── NCBI_Protein.mod.dtd │ │ │ │ ├── NCBI_Pub.mod.dtd │ │ │ │ ├── NCBI_RNA.mod.dtd │ │ │ │ ├── NCBI_Rsite.mod.dtd │ │ │ │ ├── NCBI_SeqTable.mod.dtd │ │ │ │ ├── NCBI_Seqalign.mod.dtd │ │ │ │ ├── NCBI_Seqfeat.mod.dtd │ │ │ │ ├── NCBI_Seqloc.mod.dtd │ │ │ │ ├── NCBI_Seqres.mod.dtd │ │ │ │ ├── NCBI_Seqset.dtd │ │ │ │ ├── NCBI_Seqset.mod.dtd │ │ │ │ ├── NCBI_Sequence.mod.dtd │ │ │ │ ├── NCBI_TSeq.dtd │ │ │ │ ├── NCBI_TSeq.mod.dtd │ │ │ │ ├── NCBI_TxInit.mod.dtd │ │ │ │ ├── PDB_General.mod.dtd │ │ │ │ ├── PIR_General.mod.dtd │ │ │ │ ├── PRF_General.mod.dtd │ │ │ │ ├── SP_General.mod.dtd │ │ │ │ ├── XHTMLtablesetup.ent │ │ │ │ ├── archivearticle.dtd │ │ │ │ ├── archivecustom-classes.ent │ │ │ │ ├── archivecustom-mixes.ent │ │ │ │ ├── archivecustom-models.ent │ │ │ │ ├── archivecustom-modules.ent │ │ │ │ ├── articlemeta.ent │ │ │ │ ├── backmatter.ent │ │ │ │ ├── bookdoc_100301.dtd │ │ │ │ ├── bookdoc_110101.dtd │ │ │ │ ├── chars.ent │ │ │ │ ├── common.ent │ │ │ │ ├── default-classes.ent │ │ │ │ ├── default-mixes.ent │ │ │ │ ├── display.ent │ │ │ │ ├── eInfo_020511.dtd │ │ │ │ ├── eLink_020511.dtd │ │ │ │ ├── eLink_090910.dtd │ │ │ │ ├── eLink_101123.dtd │ │ │ │ ├── ePost_020511.dtd │ │ │ │ ├── eSearch_020511.dtd │ │ │ │ ├── eSpell.dtd │ │ │ │ ├── eSummary_041029.dtd │ │ │ │ ├── egquery.dtd │ │ │ │ ├── elink_020122.dtd │ │ │ │ ├── format.ent │ │ │ │ ├── htmltable.dtd │ │ │ │ ├── isoamsa.ent │ │ │ │ ├── isoamsb.ent │ │ │ │ ├── isoamsc.ent │ │ │ │ ├── isoamsn.ent │ │ │ │ ├── isoamso.ent │ │ │ │ ├── isoamsr.ent │ │ │ │ ├── isobox.ent │ │ │ │ ├── isocyr1.ent │ │ │ │ ├── isocyr2.ent │ │ │ │ ├── isodia.ent │ │ │ │ ├── isogrk1.ent │ │ │ │ ├── isogrk2.ent │ │ │ │ ├── isogrk3.ent │ │ │ │ ├── isogrk4.ent │ │ │ │ ├── isolat1.ent │ │ │ │ ├── isolat2.ent │ │ │ │ ├── isomfrk.ent │ │ │ │ ├── isomopf.ent │ │ │ │ ├── isomscr.ent │ │ │ │ ├── isonum.ent │ │ │ │ ├── isopub.ent │ │ │ │ ├── isotech.ent │ │ │ │ ├── journalmeta.ent │ │ │ │ ├── link.ent │ │ │ │ ├── list.ent │ │ │ │ ├── math.ent │ │ │ │ ├── mathml2-qname-1.mod │ │ │ │ ├── mathml2.dtd │ │ │ │ ├── mathmlsetup.ent │ │ │ │ ├── mmlalias.ent │ │ │ │ ├── mmlextra.ent │ │ │ │ ├── modules.ent │ │ │ │ ├── nlm-articleset-2.0.dtd │ │ │ │ ├── nlmcommon_011101.dtd │ │ │ │ ├── nlmcommon_080101.dtd │ │ │ │ ├── nlmcommon_090101.dtd │ │ │ │ ├── nlmmedline_011101.dtd │ │ │ │ ├── nlmmedline_080101.dtd │ │ │ │ ├── nlmmedline_090101.dtd │ │ │ │ ├── nlmmedlinecitation_011101.dtd │ │ │ │ ├── nlmmedlinecitation_080101.dtd │ │ │ │ ├── nlmmedlinecitation_090101.dtd │ │ │ │ ├── nlmmedlinecitationset_100101.dtd │ │ │ │ ├── nlmmedlinecitationset_100301.dtd │ │ │ │ ├── nlmmedlinecitationset_110101.dtd │ │ │ │ ├── nlmserials_080101.dtd │ │ │ │ ├── nlmserials_100101.dtd │ │ │ │ ├── nlmsharedcatcit_080101.dtd │ │ │ │ ├── nlmsharedcatcit_090101.dtd │ │ │ │ ├── notat.ent │ │ │ │ ├── para.ent │ │ │ │ ├── phrase.ent │ │ │ │ ├── pmc-1.dtd │ │ │ │ ├── pubmed_020114.dtd │ │ │ │ ├── pubmed_080101.dtd │ │ │ │ ├── pubmed_090101.dtd │ │ │ │ ├── pubmed_100101.dtd │ │ │ │ ├── pubmed_100301.dtd │ │ │ │ ├── pubmed_110101.dtd │ │ │ │ ├── references.ent │ │ │ │ ├── section.ent │ │ │ │ ├── taxon.dtd │ │ │ │ └── xmlspecchars.ent │ │ │ ├── Parser.py │ │ │ └── __init__.py │ │ ├── ExPASy │ │ │ ├── Enzyme.py │ │ │ ├── Prodoc.py │ │ │ ├── Prosite.py │ │ │ ├── ScanProsite.py │ │ │ └── __init__.py │ │ ├── FSSP │ │ │ ├── FSSPTools.py │ │ │ ├── __init__.py │ │ │ └── fssp_rec.py │ │ ├── File.py │ │ ├── GA │ │ │ ├── Crossover │ │ │ │ ├── General.py │ │ │ │ ├── GeneralPoint.py │ │ │ │ ├── Point.py │ │ │ │ ├── TwoPoint.py │ │ │ │ ├── Uniform.py │ │ │ │ └── __init__.py │ │ │ ├── Evolver.py │ │ │ ├── Mutation │ │ │ │ ├── General.py │ │ │ │ ├── Simple.py │ │ │ │ └── __init__.py │ │ │ ├── Organism.py │ │ │ ├── Repair │ │ │ │ ├── Stabilizing.py │ │ │ │ └── __init__.py │ │ │ ├── Selection │ │ │ │ ├── Abstract.py │ │ │ │ ├── Diversity.py │ │ │ │ ├── RouletteWheel.py │ │ │ │ ├── Tournament.py │ │ │ │ └── __init__.py │ │ │ └── __init__.py │ │ ├── GenBank │ │ │ ├── LocationParser.py │ │ │ ├── Record.py │ │ │ ├── Scanner.py │ │ │ ├── __init__.py │ │ │ └── utils.py │ │ ├── Geo │ │ │ ├── Record.py │ │ │ └── __init__.py │ │ ├── Graphics │ │ │ ├── BasicChromosome.py │ │ │ ├── Comparative.py │ │ │ ├── DisplayRepresentation.py │ │ │ ├── Distribution.py │ │ │ ├── GenomeDiagram │ │ │ │ ├── _AbstractDrawer.py │ │ │ │ ├── _CircularDrawer.py │ │ │ │ ├── _Colors.py │ │ │ │ ├── _Diagram.py │ │ │ │ ├── _Feature.py │ │ │ │ ├── _FeatureSet.py │ │ │ │ ├── _Graph.py │ │ │ │ ├── _GraphSet.py │ │ │ │ ├── _LinearDrawer.py │ │ │ │ ├── _Track.py │ │ │ │ └── __init__.py │ │ │ └── __init__.py │ │ ├── HMM │ │ │ ├── DynamicProgramming.py │ │ │ ├── MarkovModel.py │ │ │ ├── Trainer.py │ │ │ ├── Utilities.py │ │ │ └── __init__.py │ │ ├── HotRand.py │ │ ├── Index.py │ │ ├── KDTree │ │ │ ├── KDTree.py │ │ │ ├── _CKDTree.py │ │ │ └── __init__.py │ │ ├── KEGG │ │ │ ├── Compound │ │ │ │ └── __init__.py │ │ │ ├── Enzyme │ │ │ │ └── __init__.py │ │ │ ├── Map │ │ │ │ └── __init__.py │ │ │ └── __init__.py │ │ ├── LogisticRegression.py │ │ ├── MarkovModel.py │ │ ├── MaxEntropy.py │ │ ├── Medline │ │ │ └── __init__.py │ │ ├── Motif │ │ │ ├── Applications │ │ │ │ ├── _AlignAce.py │ │ │ │ └── __init__.py │ │ │ ├── Parsers │ │ │ │ ├── AlignAce.py │ │ │ │ ├── MAST.py │ │ │ │ ├── MEME.py │ │ │ │ └── __init__.py │ │ │ ├── Thresholds.py │ │ │ ├── _Motif.py │ │ │ ├── __init__.py │ │ │ └── _pwm.py │ │ ├── NMR │ │ │ ├── NOEtools.py │ │ │ ├── __init__.py │ │ │ └── xpktools.py │ │ ├── NaiveBayes.py │ │ ├── NeuralNetwork │ │ │ ├── BackPropagation │ │ │ │ ├── Layer.py │ │ │ │ ├── Network.py │ │ │ │ └── __init__.py │ │ │ ├── Gene │ │ │ │ ├── Motif.py │ │ │ │ ├── Pattern.py │ │ │ │ ├── Schema.py │ │ │ │ ├── Signature.py │ │ │ │ └── __init__.py │ │ │ ├── StopTraining.py │ │ │ ├── Training.py │ │ │ └── __init__.py │ │ ├── Nexus │ │ │ ├── Nexus.py │ │ │ ├── Nodes.py │ │ │ ├── Trees.py │ │ │ ├── __init__.py │ │ │ └── cnexus.py │ │ ├── PDB │ │ │ ├── AbstractPropertyMap.py │ │ │ ├── Atom.py │ │ │ ├── Chain.py │ │ │ ├── DSSP.py │ │ │ ├── Dice.py │ │ │ ├── Entity.py │ │ │ ├── FragmentMapper.py │ │ │ ├── HSExposure.py │ │ │ ├── MMCIF2Dict.py │ │ │ ├── MMCIFParser.py │ │ │ ├── Model.py │ │ │ ├── NACCESS.py │ │ │ ├── NeighborSearch.py │ │ │ ├── PDBExceptions.py │ │ │ ├── PDBIO.py │ │ │ ├── PDBList.py │ │ │ ├── PDBParser.py │ │ │ ├── PSEA.py │ │ │ ├── Polypeptide.py │ │ │ ├── Residue.py │ │ │ ├── ResidueDepth.py │ │ │ ├── Selection.py │ │ │ ├── Structure.py │ │ │ ├── StructureAlignment.py │ │ │ ├── StructureBuilder.py │ │ │ ├── Superimposer.py │ │ │ ├── Vector.py │ │ │ ├── __init__.py │ │ │ ├── mmCIF │ │ │ │ └── __init__.py │ │ │ └── parse_pdb_header.py │ │ ├── ParserSupport.py │ │ ├── Parsers │ │ │ ├── __init__.py │ │ │ └── spark.py │ │ ├── Pathway │ │ │ ├── Rep │ │ │ │ ├── Graph.py │ │ │ │ ├── HashSet.py │ │ │ │ ├── MultiGraph.py │ │ │ │ └── __init__.py │ │ │ └── __init__.py │ │ ├── Phylo │ │ │ ├── Applications │ │ │ │ ├── _Phyml.py │ │ │ │ └── __init__.py │ │ │ ├── BaseTree.py │ │ │ ├── Newick.py │ │ │ ├── NewickIO.py │ │ │ ├── NexusIO.py │ │ │ ├── PAML │ │ │ │ ├── __init__.py │ │ │ │ ├── _paml.py │ │ │ │ ├── _parse_baseml.py │ │ │ │ ├── _parse_codeml.py │ │ │ │ ├── _parse_yn00.py │ │ │ │ ├── baseml.py │ │ │ │ ├── chi2.py │ │ │ │ ├── codeml.py │ │ │ │ └── yn00.py │ │ │ ├── PhyloXML.py │ │ │ ├── PhyloXMLIO.py │ │ │ ├── __init__.py │ │ │ ├── _io.py │ │ │ ├── _sugar.py │ │ │ └── _utils.py │ │ ├── PopGen │ │ │ ├── Async │ │ │ │ ├── Local.py │ │ │ │ └── __init__.py │ │ │ ├── FDist │ │ │ │ ├── Async.py │ │ │ │ ├── Controller.py │ │ │ │ ├── Utils.py │ │ │ │ └── __init__.py │ │ │ ├── GenePop │ │ │ │ ├── Controller.py │ │ │ │ ├── EasyController.py │ │ │ │ ├── FileParser.py │ │ │ │ ├── LargeFileParser.py │ │ │ │ ├── Utils.py │ │ │ │ └── __init__.py │ │ │ ├── SimCoal │ │ │ │ ├── Async.py │ │ │ │ ├── Cache.py │ │ │ │ ├── Controller.py │ │ │ │ ├── Template.py │ │ │ │ ├── __init__.py │ │ │ │ └── data │ │ │ │ │ ├── bottle.par │ │ │ │ │ ├── decline_lambda.par │ │ │ │ │ ├── decline_split.par │ │ │ │ │ ├── island.par │ │ │ │ │ ├── simple.par │ │ │ │ │ ├── split_island.par │ │ │ │ │ ├── split_ssm_1d.par │ │ │ │ │ ├── split_ssm_2d.par │ │ │ │ │ ├── ssm_1d.par │ │ │ │ │ └── ssm_2d.par │ │ │ └── __init__.py │ │ ├── Restriction │ │ │ ├── PrintFormat.py │ │ │ ├── RanaConfig.py │ │ │ ├── Restriction.py │ │ │ ├── Restriction_Dictionary.py │ │ │ ├── _Update │ │ │ │ ├── RestrictionCompiler.py │ │ │ │ ├── Update.py │ │ │ │ └── __init__.py │ │ │ └── __init__.py │ │ ├── SCOP │ │ │ ├── Cla.py │ │ │ ├── Des.py │ │ │ ├── Dom.py │ │ │ ├── Hie.py │ │ │ ├── Raf.py │ │ │ ├── Residues.py │ │ │ └── __init__.py │ │ ├── SVDSuperimposer │ │ │ ├── SVDSuperimposer.py │ │ │ └── __init__.py │ │ ├── Search.py │ │ ├── Seq.py │ │ ├── SeqFeature.py │ │ ├── SeqIO │ │ │ ├── AbiIO.py │ │ │ ├── AceIO.py │ │ │ ├── FastaIO.py │ │ │ ├── IgIO.py │ │ │ ├── InsdcIO.py │ │ │ ├── Interfaces.py │ │ │ ├── PhdIO.py │ │ │ ├── PirIO.py │ │ │ ├── QualityIO.py │ │ │ ├── SeqXmlIO.py │ │ │ ├── SffIO.py │ │ │ ├── SwissIO.py │ │ │ ├── TabIO.py │ │ │ ├── UniprotIO.py │ │ │ ├── __init__.py │ │ │ ├── _convert.py │ │ │ └── _index.py │ │ ├── SeqRecord.py │ │ ├── SeqUtils │ │ │ ├── CheckSum.py │ │ │ ├── CodonUsage.py │ │ │ ├── CodonUsageIndices.py │ │ │ ├── IsoelectricPoint.py │ │ │ ├── MeltingTemp.py │ │ │ ├── ProtParam.py │ │ │ ├── ProtParamData.py │ │ │ ├── __init__.py │ │ │ └── lcc.py │ │ ├── Sequencing │ │ │ ├── Ace.py │ │ │ ├── Applications │ │ │ │ ├── _Novoalign.py │ │ │ │ └── __init__.py │ │ │ ├── Phd.py │ │ │ └── __init__.py │ │ ├── Statistics │ │ │ ├── __init__.py │ │ │ └── lowess.py │ │ ├── SubsMat │ │ │ ├── FreqTable.py │ │ │ ├── MatrixInfo.py │ │ │ └── __init__.py │ │ ├── SwissProt │ │ │ ├── KeyWList.py │ │ │ └── __init__.py │ │ ├── UniGene │ │ │ ├── UniGene.py │ │ │ └── __init__.py │ │ ├── Wise │ │ │ ├── __init__.py │ │ │ ├── dnal.py │ │ │ └── psw.py │ │ ├── __init__.py │ │ ├── _py3k.py │ │ ├── cpairwise2.py │ │ ├── kNN.py │ │ ├── pairwise2.py │ │ ├── trie.py │ │ └── triefind.py │ ├── README.rst │ ├── last.py │ ├── last_helper.py │ ├── lastal │ ├── lastdb │ ├── lastex │ ├── patch │ └── test │ │ ├── 4241-CDS.fasta │ │ ├── 4241-CDS.prj │ │ ├── 4241-CDS0.bck │ │ ├── 4241-CDS0.des │ │ ├── 4241-CDS0.prj │ │ ├── 4241-CDS0.sds │ │ ├── 4241-CDS0.ssp │ │ ├── 4241-CDS0.suf │ │ ├── 4241-CDS0.tis │ │ ├── 4242-CDS.fasta │ │ ├── README │ │ └── test.out ├── nwserver.py ├── quota-alignment │ ├── .gitignore │ ├── README.rst │ ├── box_utils.py │ ├── cluster_utils.py │ ├── grimm │ ├── grouper.py │ ├── lp_solvers.py │ ├── maf_utils.py │ ├── quota_align.py │ ├── run.sh │ └── scripts │ │ ├── bed_utils.py │ │ ├── blast_plot.py │ │ ├── blast_to_raw.py │ │ ├── gff_to_bed.py │ │ ├── lis.py │ │ ├── qa_plot.py │ │ ├── qa_to_pairs.py │ │ ├── run.sh │ │ └── synteny_score.py ├── snp_search │ ├── Makefile │ ├── snp_search │ └── snp_search.cpp └── spa.pl ├── bower.json ├── make_perl.sh ├── modules.txt ├── modules ├── Accessory │ ├── MANIFEST │ ├── Makefile.PL │ ├── lib │ │ └── CoGe │ │ │ └── Accessory │ │ │ ├── Annotation.pm │ │ │ ├── BisQue.pm │ │ │ ├── Entrez.pm │ │ │ ├── GBlite.pm │ │ │ ├── GenBank.pm │ │ │ ├── GenBank │ │ │ └── Feature.pm │ │ │ ├── GenomeThreader_report.pm │ │ │ ├── IRODS.pm │ │ │ ├── SynMap_report.pm │ │ │ ├── TDS.pm │ │ │ ├── Tile │ │ │ └── Cache.pm │ │ │ ├── Utils.pm │ │ │ ├── Web.pm │ │ │ ├── bl2seq_report.pm │ │ │ ├── blast_report.pm │ │ │ ├── blastz_report.pm │ │ │ ├── blastz_report │ │ │ ├── segment.pm │ │ │ └── seq.pm │ │ │ ├── chaos_report.pm │ │ │ ├── dialign_report.pm │ │ │ ├── dialign_report │ │ │ └── anchors.pm │ │ │ ├── genetic_code.pm │ │ │ ├── histogram.pm │ │ │ ├── lagan_report.pm │ │ │ └── parse_report │ │ │ └── HSP.pm │ └── t │ │ ├── 001_load.t │ │ └── url.t ├── Algos │ ├── Codeml │ │ ├── MANIFEST │ │ ├── Makefile.PL │ │ ├── lib │ │ │ └── CoGe │ │ │ │ └── Algos │ │ │ │ └── Codeml.pm │ │ └── t │ │ │ ├── 001_load.t │ │ │ └── test.phy │ ├── KsCalc │ │ ├── MANIFEST │ │ ├── Makefile.PL │ │ ├── lib │ │ │ └── CoGe │ │ │ │ └── Algos │ │ │ │ └── KsCalc.pm │ │ ├── scripts │ │ │ └── test.pl │ │ └── t │ │ │ └── 001_load.t │ ├── Makefile.PL │ ├── Pairwise │ │ ├── MANIFEST │ │ ├── Makefile.PL │ │ ├── lib │ │ │ └── CoGe │ │ │ │ └── Algos │ │ │ │ └── Pairwise.pm │ │ ├── scripts │ │ │ ├── convert_matrix.pl │ │ │ └── test.pl │ │ └── t │ │ │ └── 001_load.t │ └── PopGen │ │ ├── MANIFEST │ │ ├── Makefile.PL │ │ └── lib │ │ └── CoGe │ │ └── Algos │ │ └── PopGen │ │ ├── Diversity.pm │ │ ├── FileFormats.pm │ │ └── Stats.pm ├── Core │ ├── MANIFEST │ ├── Makefile.PL │ └── lib │ │ └── CoGe │ │ └── Core │ │ ├── Chromosomes.pm │ │ ├── Experiment.pm │ │ ├── Favorites.pm │ │ ├── Feature.pm │ │ ├── Genome.pm │ │ ├── Item.pm │ │ ├── Metadata.pm │ │ ├── Notebook.pm │ │ ├── Search.pm │ │ ├── Sequence.pm │ │ └── Storage.pm ├── Database │ ├── MANIFEST │ ├── Makefile.PL │ ├── lib │ │ ├── CoGeDBI.pm │ │ ├── CoGeX.pm │ │ ├── CoGeX │ │ │ ├── Result │ │ │ │ ├── AnnotationType.pm │ │ │ │ ├── AnnotationTypeGroup.pm │ │ │ │ ├── DataSource.pm │ │ │ │ ├── Dataset.pm │ │ │ │ ├── DatasetConnector.pm │ │ │ │ ├── Experiment.pm │ │ │ │ ├── ExperimentAnnotation.pm │ │ │ │ ├── ExperimentType.pm │ │ │ │ ├── ExperimentTypeConnector.pm │ │ │ │ ├── FavoriteConnector.pm │ │ │ │ ├── Feature.pm │ │ │ │ ├── FeatureAnnotation.pm │ │ │ │ ├── FeatureName.pm │ │ │ │ ├── FeatureType.pm │ │ │ │ ├── Genome.pm │ │ │ │ ├── GenomeAnnotation.pm │ │ │ │ ├── GenomicSequence.pm │ │ │ │ ├── GenomicSequenceType.pm │ │ │ │ ├── Image.pm │ │ │ │ ├── Job.pm │ │ │ │ ├── List.pm │ │ │ │ ├── ListAnnotation.pm │ │ │ │ ├── ListConnector.pm │ │ │ │ ├── ListType.pm │ │ │ │ ├── Location.pm │ │ │ │ ├── Log.pm │ │ │ │ ├── Organism.pm │ │ │ │ ├── Role.pm │ │ │ │ ├── User.pm │ │ │ │ ├── UserConnector.pm │ │ │ │ ├── UserGroup.pm │ │ │ │ ├── UserSession.pm │ │ │ │ └── WebPreferences.pm │ │ │ └── ResultSet │ │ │ │ ├── Dataset.pm │ │ │ │ ├── Experiment.pm │ │ │ │ ├── Feature.pm │ │ │ │ ├── FeatureAnnotation.pm │ │ │ │ ├── FeatureName.pm │ │ │ │ ├── Genome.pm │ │ │ │ ├── GenomicSequenceType.pm │ │ │ │ ├── List.pm │ │ │ │ └── Organism.pm │ │ ├── DBIxProfiler.pm │ │ └── FastBit.pm │ └── t │ │ ├── 001_load.t │ │ ├── 002_feature_by_id.t │ │ ├── 003_organism_by_name.t │ │ ├── 004_features_from_dataset.t │ │ ├── 005_feature_by_organism.t │ │ ├── 006_genome_sequence_datasetid.t │ │ ├── 007_protein_sequence_from_feature.t │ │ ├── 008_genomic_sequence_from_feature.t │ │ ├── 009_feature_from_dataset_repeated.t │ │ ├── 010_features_in_region.t │ │ ├── 011_features_in_region_split.t │ │ ├── 012_feature_in_region_locs.t │ │ ├── 013_features_in_region_ecoli.t │ │ ├── 014_get_seq.t │ │ ├── asdf.fasta │ │ ├── asdf.fasta.nhr │ │ ├── asdf.fasta.nin │ │ ├── asdf.fasta.nnd │ │ ├── asdf.fasta.nni │ │ ├── asdf.fasta.nsd │ │ ├── asdf.fasta.nsi │ │ └── asdf.fasta.nsq ├── ECNCS │ ├── MANIFEST │ ├── Makefile.PL │ ├── lib │ │ └── CoGe │ │ │ ├── ECNCS.pm │ │ │ └── ECNCS │ │ │ ├── DB.pm │ │ │ └── DB │ │ │ ├── Algorithm.pm │ │ │ ├── Algorithm_data.pm │ │ │ ├── Algorithm_run.pm │ │ │ ├── Author.pm │ │ │ ├── Classification.pm │ │ │ ├── Data_mask.pm │ │ │ ├── Ecncs.pm │ │ │ ├── Location.pm │ │ │ ├── Spike.pm │ │ │ └── Status.pm │ └── t │ │ ├── 001_load.t │ │ ├── 002_load.t │ │ ├── 003_load.t │ │ ├── 004_load.t │ │ ├── 005_load.t │ │ ├── 006_load.t │ │ ├── 007_load.t │ │ ├── 008_load.t │ │ ├── 009_load.t │ │ ├── 010_load.t │ │ ├── 011_load.t │ │ └── 012_load.t ├── Exception │ ├── MANIFEST │ ├── Makefile.PL │ └── lib │ │ └── CoGe │ │ └── Exception │ │ ├── AccessDenied.pm │ │ ├── Generic.pm │ │ ├── ItemNotFound.pm │ │ └── MissingField.pm ├── Graphics │ ├── MANIFEST │ ├── Makefile.PL │ ├── lib │ │ └── CoGe │ │ │ ├── Graphics.pm │ │ │ └── Graphics │ │ │ ├── Chromosome.pm │ │ │ ├── Feature.pm │ │ │ ├── Feature │ │ │ ├── AminoAcid.pm │ │ │ ├── Block.pm │ │ │ ├── Circle.pm │ │ │ ├── Diamond.pm │ │ │ ├── Domain.pm │ │ │ ├── Exon_motifs.pm │ │ │ ├── Flag.pm │ │ │ ├── GAGA.pm │ │ │ ├── GBox.pm │ │ │ ├── Gene.pm │ │ │ ├── HSP.pm │ │ │ ├── Link.pm │ │ │ ├── NucTide.pm │ │ │ ├── Outline.pm │ │ │ ├── Quant.pm │ │ │ └── Sigma54.pm │ │ │ └── GenomeView.pm │ └── t │ │ ├── 001_load.t │ │ └── 002_load.t ├── JEX │ ├── MANIFEST │ ├── Makefile.PL │ └── lib │ │ └── CoGe │ │ └── JEX │ │ ├── Jex.pm │ │ └── Workflow.pm ├── MANIFEST ├── Makefile.PL ├── Pipelines │ ├── MANIFEST │ ├── Makefile.PL │ └── lib │ │ └── CoGe │ │ ├── Builder │ │ ├── Alignment │ │ │ ├── Aligner.pm │ │ │ ├── BWA.pm │ │ │ ├── BWAmeth.pm │ │ │ ├── Bismark.pm │ │ │ ├── Bowtie.pm │ │ │ ├── GSNAP.pm │ │ │ ├── HISAT2.pm │ │ │ └── Tophat.pm │ │ ├── Buildable.pm │ │ ├── CommonTasks.pm │ │ ├── Data │ │ │ └── Extractor.pm │ │ ├── Export │ │ │ ├── Experiment.pm │ │ │ ├── Fasta.pm │ │ │ ├── Genome.pm │ │ │ └── Gff.pm │ │ ├── Expression │ │ │ ├── Analyzer.pm │ │ │ └── Cufflinks.pm │ │ ├── Load │ │ │ ├── Annotation.pm │ │ │ ├── BatchExperiment.pm │ │ │ ├── Experiment.pm │ │ │ ├── Genome.pm │ │ │ └── SRA.pm │ │ ├── Methylation │ │ │ ├── Analyzer.pm │ │ │ ├── BWAmeth.pm │ │ │ ├── Bismark.pm │ │ │ └── Metaplot.pm │ │ ├── PopGen │ │ │ └── SummaryStats.pm │ │ ├── Protein │ │ │ └── ChIPseq.pm │ │ ├── SNP │ │ │ ├── Analyzer.pm │ │ │ ├── CoGeSNPs.pm │ │ │ ├── GATK.pm │ │ │ ├── Merge.pm │ │ │ ├── Platypus.pm │ │ │ └── Samtools.pm │ │ ├── Tools │ │ │ ├── CoGeBlast.pm │ │ │ ├── PercentGCAT.pm │ │ │ ├── Pseudoassembly.pm │ │ │ ├── SynMap.pm │ │ │ ├── SynMap3D.pm │ │ │ └── SynMapN.pm │ │ └── Trimming │ │ │ ├── BBDuk.pm │ │ │ ├── Cutadapt.pm │ │ │ ├── TrimGalore.pm │ │ │ ├── Trimmer.pm │ │ │ └── Trimmomatic.pm │ │ ├── Factory │ │ ├── PipelineFactory.pm │ │ └── RequestFactory.pm │ │ └── Request │ │ ├── CoGeBlast.pm │ │ ├── Empty.pm │ │ ├── Experiment.pm │ │ ├── ExperimentAnalysis.pm │ │ ├── Genome.pm │ │ ├── NExperiments.pm │ │ ├── NGenomes.pm │ │ ├── Request.pm │ │ └── TwoGenomes.pm └── Services │ ├── MANIFEST │ ├── Makefile.PL │ └── lib │ └── CoGe │ └── Services │ ├── API │ ├── Annotations.pm │ ├── Dataset.pm │ ├── Download.pm │ ├── Experiment.pm │ ├── FTP.pm │ ├── Feature.pm │ ├── Genome.pm │ ├── Group.pm │ ├── IRODS.pm │ ├── JBrowse │ │ ├── Annotation.pm │ │ ├── Configuration.pm │ │ ├── Experiment.pm │ │ ├── GCcontent.pm │ │ ├── Genome.pm │ │ ├── Search.pm │ │ └── Sequence.pm │ ├── Job.pm │ ├── Log.pm │ ├── Notebook.pm │ ├── Organism.pm │ ├── Search.pm │ ├── Sequence.pm │ └── User.pm │ ├── Auth.pm │ └── Error.pm ├── old ├── Blank.pl ├── Blank.tmpl ├── CoGeBlast_old.pl ├── CoGe_faq.html ├── CodeFusion.pl ├── CodeFusion.tmpl ├── Experiments.pl ├── Experiments.tmpl ├── FeatID2Names.pl ├── FeatListView.pl ├── FeatListView.tmpl ├── GenomeAlign.pl ├── GenomeAlign.tmpl ├── GenomeAlign │ ├── mauve_alignment.pl │ └── progressiveMauve-muscleMatrix ├── GenomePNG.pl ├── GenomeView_old.pl ├── GenomeView_old.tmpl ├── Genomes.pl ├── Genomes.tmpl ├── GetSequence.pl ├── Groups.pl ├── Groups.tmpl ├── History.pl ├── History.tmpl ├── Jobs.pl ├── Jobs.tmpl ├── MSAView.pl ├── MSAView.tmpl ├── MotifFind.pl ├── MotifFind.tmpl ├── MotifView.pl ├── MotifView.tmpl ├── MotifViewDev.pl ├── Notebooks.pl ├── Notebooks.tmpl ├── SeqType.pl ├── SeqType.tmpl ├── Sources.pl ├── Sources.tmpl ├── SynFind_old.pl ├── SynView-papaya.pl ├── TreeView.pl ├── TreeView.tmpl ├── UserGraph.pl ├── UserGraph.tmpl ├── fastbit_query.pl ├── get_org_list.pl ├── three_dots_merge.py └── tiler.pl ├── resources ├── adapters.fa └── experiment.README.txt ├── scripts ├── README ├── add_items_to_notebook.pl ├── add_metadata_to_results.pl ├── add_workflow_result.pl ├── backup │ ├── audit_backup.pl │ ├── backup.sh │ ├── fetch.sh │ └── sync_jex_db.pl ├── chipseq │ └── homer_peaks_to_csv.pl ├── clean_up_bad_synmap.pl ├── cleanup │ ├── cleanup_staging.pl │ ├── compress_experiment_files.pl │ └── delete_genome_derivative_files.pl ├── coge2bed.pl ├── coge2bed.v2.pl ├── coge_gff.pl ├── copy_genome │ ├── copy_load_mask_genome.pl │ ├── hard_mask.pl │ ├── merge_genomes.pl │ ├── replicate_annotations.pl │ └── windowmasker ├── create_notebook.pl ├── cutadapt.pl ├── diags │ ├── add_annotations_using_dag_file.pl │ ├── clean_blastn.pl │ ├── clean_condensed.pl │ ├── clean_genomic.pl │ ├── clean_old_comparisons.pl │ ├── clean_old_filtered.pl │ ├── clean_old_images.pl │ ├── clean_old_ks_files.pl │ ├── clean_old_running.pl │ ├── clean_old_sqlite.pl │ ├── clean_qac.pl │ ├── compress_stuff.pl │ ├── gen_pairs_file.pl │ └── scrub_diags_directory.pl ├── export_NCBI_TBL.pl ├── export_experiment_or_genome.pl ├── export_features_by_type.pl ├── export_to_gff.pl ├── fasta_reheader.pl ├── filter_sam.pl ├── fix_chromosome_id.pl ├── ftp.pl ├── genbank_genome_loader.pl ├── generate_chr_fasta.pl ├── generate_results.pl ├── gff_to_bed.pl ├── irods.pl ├── link_results.pl ├── load_all_ncbi_genomes.pl ├── load_all_ncbi_microbial_complete_genomes.pl ├── load_annotation.pl ├── load_annotation_ensembl_GTF.pl ├── load_batch.pl ├── load_experiment.pl ├── load_genome.pl ├── methylation │ ├── coge-import_bismark.py │ ├── coge-import_pileometh.py │ ├── fix_chromosome_id.py │ └── makeMetaplot.pl ├── migration │ ├── index_genomes.pl │ └── update_exp_count.pl ├── normalize_bed.pl ├── old │ ├── BGF_annotation_loader.pl │ ├── add_chr_to_dataset.pl │ ├── add_dataset_to_dataset_group.pl │ ├── add_gene_features_to_dataset.pl │ ├── add_user.pl │ ├── break_fasta_2_chr.pl │ ├── check_ncbi_genome_lengths.pl │ ├── clone_dataset.pl │ ├── clone_empty_genome.pl │ ├── code_fusion_for_org.pl │ ├── codon_usage.pl │ ├── coge_mauve_alignment.pl │ ├── convert_to_gene_order.pl │ ├── create_dataset.pl │ ├── create_dataset_group.pl │ ├── dataset_summary_for_organism.pl │ ├── delete_dataset.pl │ ├── delete_dataset_group.pl │ ├── delete_features.pl │ ├── delete_features_for_dataset.pl │ ├── delete_features_for_organism.pl │ ├── delete_organism.pl │ ├── delete_organisms_with_no_dataset_groups.pl │ ├── dotplot_dots.pl │ ├── export_to_bed.pl │ ├── export_to_flat.pl │ ├── export_to_simple.pl │ ├── fasta_genome_loader.pl │ ├── feature_merge.pl │ ├── find_SNPs.pl │ ├── find_datasets_with_no_sequence.pl │ ├── find_duplicate_datasets.pl │ ├── find_gene_annotations.pl │ ├── find_organisms_with_no_dataset.pl │ ├── find_tRNAs_with_aragorn.pl │ ├── fix_duplicate_organism_entries.pl │ ├── fix_feature_names.pl │ ├── fix_locations_for_organism.pl │ ├── gen_fasta_file_for_CDS_for_blast.pl │ ├── genbank_contig_loader.pl │ ├── genbank_genome_loader.pl │ ├── genbank_genome_loader_new.pl │ ├── generate_dataset_groups.pl │ ├── get_by_name.pl │ ├── get_codon_usage_for_org.pl │ ├── get_features_for_genome.pl │ ├── get_features_for_organism.pl │ ├── get_features_locs.pl │ ├── get_genome_for_organism.pl │ ├── get_genomic_sequence_for_organism.pl │ ├── get_org_list.pl │ ├── get_tRNA_usage_for_org.pl │ ├── get_wobble_count_for_org.pl │ ├── gff_annotation_loader.pl │ ├── gff_annotation_loader_msu_rice.pl │ ├── gff_annotation_loader_phytozome.pl │ ├── load_TIGR_XML.pl │ ├── load_additional_annotations.pl │ ├── load_all_ncbi_genomes_bioprojects.pl │ ├── load_custom_genbank.pl │ ├── load_domains.pl │ ├── load_genome_and_copy_features.pl │ ├── load_jgi_go.pl │ ├── load_tRNA_scan_models.pl │ ├── load_tab_delimited_annotation.pl │ ├── load_tabdelim_features_for_dataset.pl │ ├── migrate_coge5.5.pl │ ├── migrate_coge5.pl │ ├── migrate_genomes.pl │ ├── polyMFind.pl │ ├── poplar │ │ ├── fix_poplar.pl │ │ ├── new_names_to_old.pl │ │ ├── poplar_order.pl │ │ └── poplar_sequence.pl │ ├── prodigal_gff_annotation_loader.pl │ ├── qteller.pl │ ├── remove_duplicate_ncbi_datasets.pl │ ├── replicate_annotations.pl │ ├── replicate_dataset_features.pl │ ├── replicate_genome.pl │ ├── replicate_genome_between_coge_installations.pl │ ├── simle2sqlite.py │ ├── syntenic_annotation_lift_over.pl │ ├── update_feature_names_to_add_primary_name.pl │ └── update_ncbi_dataset_links.pl ├── parse_cufflinks.py ├── percent_gc_at.py ├── pileup_SNPs.pl ├── pileup_to_bed.pl ├── popgen │ └── sumstats.pl ├── process_fasta.pl ├── query_analytics.py ├── send_email.pl ├── sort_fasta.pl ├── synmap │ ├── blast2bed.pl │ ├── dag_tools.py │ ├── dotplot.py │ ├── dotplot_dots.py │ ├── fractionation_bias.py │ ├── gene_order.py │ ├── generate_fasta.pl │ ├── gevo_links.pl │ ├── kscalc.pl │ ├── order_contigs_to_chromosome.pl │ ├── process_dups.pl │ ├── quota_align_coverage.pl │ ├── quota_align_merge.pl │ ├── svgfig.py │ └── synmerge_3.py ├── system_stats.pl ├── tophat.pl ├── utils │ ├── alert_on_filesystem_full.pl │ ├── audit_coge5.5.pl │ ├── audit_datasets.pl │ ├── check_coge_data_dirs.pl │ ├── gen_fake_data.pl │ └── update-jobs.py └── validate_fastq.pl ├── setup.sh ├── tests ├── JEX │ └── validate_workflow.pl └── api │ ├── cogeblast.robot │ ├── data │ ├── experiment_add.json │ ├── experiment_fetch.json │ ├── genome_add.json │ ├── genome_add_16911.json │ ├── genome_fetch.json │ ├── load_annotation.json │ ├── notebook_add.json │ └── notebook_fetch.json │ ├── experiments.robot │ ├── export.robot │ ├── genomes.robot │ ├── notebooks.robot │ ├── organisms.robot │ ├── performance.robot │ ├── resource.robot │ ├── run_tests.sh │ └── search.robot ├── tmpl ├── Account.tmpl ├── Admin.tmpl ├── CoGeAlign.tmpl ├── CoGeBlast.tmpl ├── CoGeBlast_coge.tmpl ├── CoGeBlast_ncbi.tmpl ├── CodeOn.tmpl ├── ExperimentList.tmpl ├── ExperimentView.tmpl ├── FastaView.tmpl ├── FeatList.tmpl ├── FeatMap.tmpl ├── FeatView.tmpl ├── GEvo-old.tmpl ├── GEvo.tmpl ├── GEvo_direct.tmpl ├── GenomeInfo.tmpl ├── GenomeList.tmpl ├── GenomeView.tmpl ├── GroupView.tmpl ├── HSPView.tmpl ├── LoadAnnotation.tmpl ├── LoadBatch.tmpl ├── LoadExperiment.tmpl ├── LoadGenome.tmpl ├── MatrixView.tmpl ├── NotebookView.tmpl ├── OrganismView.tmpl ├── PopGen.tmpl ├── Project.tmpl ├── SearchResults.tmpl ├── SeqView.tmpl ├── SynFind.tmpl ├── SynMap.tmpl ├── SynMap3D.tmpl ├── SynMapN.tmpl ├── SynSub.tmpl ├── Taxonomy.tmpl ├── User.tmpl ├── box.tmpl ├── embedded_page.tmpl ├── footer.tmpl ├── generic_page.tmpl ├── header.tmpl ├── header_includes.tmpl ├── index.tmpl ├── partials │ ├── organism_menu.tmpl │ ├── synmap_results.tmpl │ └── user_common.tmpl ├── tRNAView.tmpl └── widgets │ ├── AdminOnly.tmpl │ ├── Annotations.tmpl │ ├── Certified.tmpl │ ├── Dotplot.tmpl │ ├── FileSelect.tmpl │ ├── GenomeSelect.tmpl │ ├── JBrowse.tmpl │ ├── Login.tmpl │ ├── Overlay.tmpl │ ├── Progress.tmpl │ ├── Spinner.tmpl │ ├── Splash.tmpl │ ├── Wizard.tmpl │ ├── experiment_info_table.tmpl │ └── pipeline-options.tmpl └── web ├── .htaccess ├── Account.pl ├── Admin.pl ├── CoGeAlign.pl ├── CoGeBlast.pl ├── CodeOn.pl ├── DirSelect.pl ├── DisplayMessage.pl ├── Error.pl ├── ExperimentList.pl ├── ExperimentView.pl ├── FastaView.pl ├── FeatAnno.pl ├── FeatList.pl ├── FeatMap.pl ├── FeatView.pl ├── GEvo-old.pl ├── GEvo.pl ├── GEvo_direct.pl ├── GenomeInfo.pl ├── GenomeList.pl ├── GenomeView.pl ├── GroupView.pl ├── HSPView.pl ├── LoadAnnotation.pl ├── LoadBatch.pl ├── LoadExperiment.pl ├── LoadGenome.pl ├── MatrixView.pl ├── NotebookView.pl ├── OrganismView.pl ├── PopGen.pl ├── Project.pl ├── SSWAP ├── CoGe ├── CoGe.json ├── README └── resources │ └── FastaView │ ├── FastaView │ ├── FastaView.json │ └── README ├── SearchResults.pl ├── SeqView.pl ├── SynFind.pl ├── SynMap.pl ├── SynMap3D.pl ├── SynMapN.pl ├── SynSub.pl ├── Taxonomy.pl ├── User.pl ├── ViennaFold.pl ├── bisque_image.pl ├── bisque_viewer.pl ├── coge2bed.pl ├── coge_feature_types.sql ├── coge_mysql_schema.sql ├── css ├── coge-spinner.css ├── coge.css ├── colorpicker.css ├── dataTables.css ├── glyphicons.css ├── layout.css └── ui.tabs.css ├── export_NCBI_TBL.pl ├── favicon.ico ├── get_percent_gc_at_for_chr.pl ├── get_percent_gc_at_for_chr_json.pl ├── get_seq_for_chr.pl ├── get_seqs_for_feattype_for_genome.pl ├── gobe ├── docs │ └── textfield.html ├── flash │ ├── Gobe.hx │ ├── HSP.hx │ ├── gobe.hxml │ ├── gobe.swf │ ├── hxjson2-old │ │ ├── JSON.hx │ │ ├── JSONDecoder.hx │ │ ├── JSONEncoder.hx │ │ ├── JSONParseError.hx │ │ ├── JSONToken.hx │ │ └── JSONTokenizer.hx │ ├── hxjson2 │ │ ├── .svn-old │ │ │ ├── all-wcprops │ │ │ ├── entries │ │ │ └── text-base │ │ │ │ ├── JSON.hx.svn-base │ │ │ │ ├── JSONDecoder.hx.svn-base │ │ │ │ ├── JSONEncoder.hx.svn-base │ │ │ │ ├── JSONParseError.hx.svn-base │ │ │ │ ├── JSONToken.hx.svn-base │ │ │ │ └── JSONTokenizer.hx.svn-base │ │ ├── JSON.hx │ │ ├── JSONDecoder.hx │ │ ├── JSONEncoder.hx │ │ ├── JSONParseError.hx │ │ ├── JSONToken.hx │ │ └── JSONTokenizer.hx │ └── service.wsgi ├── gobe.py ├── index.html ├── new_images.sh ├── predict_cns.py ├── predict_cns.pyc ├── query.pl ├── static │ ├── clear_button.gif │ ├── close_button.gif │ ├── gobe-new.js │ ├── gobe.js │ ├── minus.gif │ ├── plus.gif │ ├── save.gif │ └── swfobject │ │ ├── .svn-old │ │ ├── all-wcprops │ │ ├── entries │ │ ├── prop-base │ │ │ └── expressInstall.swf.svn-base │ │ └── text-base │ │ │ ├── expressInstall.swf.svn-base │ │ │ └── swfobject.js.svn-base │ │ ├── expressInstall.swf │ │ └── swfobject.js └── tmp │ ├── GEvo_WxUonWBr.log │ ├── GEvo_WxUonWBr.sqlite │ ├── GEvo_WxUonWBr_1.png │ ├── GEvo_WxUonWBr_2.png │ └── GEvo_WxUonWBr_3.png ├── image.pl ├── index.pl ├── jbrowse_conf.json ├── js ├── coge │ ├── colors.js │ ├── contentpanel.js │ ├── datagrid.js │ ├── entrez.js │ ├── exporter.js │ ├── file-select.js │ ├── infopanel.js │ ├── logout.js │ ├── newsfeed.js │ ├── progress.js │ ├── services.js │ ├── tocpanel.js │ ├── utils.js │ ├── wikifeed.js │ └── wizard.js ├── colorpicker.js ├── filterlist.js ├── fractbias_plotter.js ├── img │ ├── blank.gif │ ├── east-mini.png │ ├── layer-switcher-maximize.png │ ├── layer-switcher-minimize.png │ ├── slider.png │ ├── west-mini.png │ ├── zoom-minus-mini.png │ ├── zoom-plus-mini.png │ └── zoombar.png ├── jquery-ui-1.12.1.custom │ ├── AUTHORS.txt │ ├── LICENSE.txt │ ├── external │ │ └── jquery │ │ │ └── jquery.js │ ├── images │ │ ├── ui-icons_444444_256x240.png │ │ ├── ui-icons_555555_256x240.png │ │ ├── ui-icons_777620_256x240.png │ │ ├── ui-icons_777777_256x240.png │ │ ├── ui-icons_cc0000_256x240.png │ │ └── ui-icons_ffffff_256x240.png │ ├── index.html │ ├── jquery-ui.css │ ├── jquery-ui.js │ ├── jquery-ui.min.js │ ├── jquery-ui.structure.css │ ├── jquery-ui.structure.min.css │ ├── jquery-ui.theme.css │ ├── jquery-ui.theme.min.css │ └── package.json ├── jquery.fileupload.js ├── jquery.tablesorter.2.0.3.js ├── jquery.tablesorter.pager.js ├── pages │ ├── admin.js │ ├── blast.js │ ├── experiment-view.js │ ├── genome-info.js │ ├── load-annotation.js │ ├── load-batch.js │ ├── load-experiment.js │ ├── load-genome.js │ ├── notebook-view.js │ ├── organism-view.js │ ├── project.js │ ├── search-results.js │ ├── synfind.js │ ├── synmap-3d.js │ ├── synmap.js │ ├── synmapn.js │ ├── user-common.js │ └── user.js ├── sswap.js ├── syn3d │ ├── VREffect_modified.js │ ├── WebVR_modified.js │ ├── modified_FlatOrbitControls.js │ ├── syn3d-0.2.js │ ├── syn3d-1.0.js │ ├── three-73.min.js │ ├── three-77.min.js │ └── threex.domevent.js ├── ui.tabs.js └── xhairs.js ├── picts ├── A.png ├── C.png ├── CoGe.svg ├── CoGeBlast.svg ├── CoGeCircuitLeaf1.svg ├── CoGePedia_icon.png ├── CoGe_logo_small.png ├── FeatView.svg ├── G.png ├── GEvo.svg ├── GenomeView.svg ├── GenomeView_GEvo-links.png ├── LoadExperiment.svg ├── LoadGenome.svg ├── LyonsLab-logo.png ├── Moore_Foundation.png ├── MotifView-logo.jpg ├── Opticon.ttf ├── Organism.svg ├── OrganismView.svg ├── PoweredbyCyverse_LogoSquare_0_0.png ├── SSWAP │ └── FastaView-SSWAP-logo.png ├── SynFind.svg ├── SynMap-inverse.svg ├── SynMap.svg ├── SynMap3d.svg ├── SynMap_AlternateColoration.svg ├── T.png ├── YouTube-icon-full_color.png ├── ajax-loader-large.gif ├── ajax-loader-medium.gif ├── ajax-loader.gif ├── animations │ ├── DNA_orbit_animated_small-side.gif │ ├── DNA_orbit_animated_small.gif │ ├── DNA_orbit_animated_small_half.gif │ ├── DNA_orbit_animated_small_third.gif │ ├── DNA_orbit_animated_small_two_third.gif │ ├── spinning_helix.gif │ └── spinning_helix_small.gif ├── arrow-down-icon.png ├── arrow-right-icon.png ├── ball.png ├── blast_table │ ├── small.gif │ ├── small_asc.gif │ └── small_desc.gif ├── buttons │ ├── CoGeBlast │ │ ├── coge_blast.png │ │ ├── ncbi_blast.png │ │ ├── ncbi_blast │ │ │ ├── active.png │ │ │ ├── inactive.png │ │ │ └── pressed.png │ │ └── ncbi_blast_new.png │ ├── GEvo │ │ ├── add.png │ │ ├── add │ │ │ ├── active.png │ │ │ ├── inactive.png │ │ │ └── pressed.png │ │ ├── add_new.png │ │ ├── clear.png │ │ ├── clear │ │ │ ├── active.png │ │ │ ├── inactive.png │ │ │ └── pressed.png │ │ ├── clear_new.png │ │ ├── expression_tree.png │ │ ├── genome_view.png │ │ ├── go.png │ │ ├── go │ │ │ ├── active.png │ │ │ ├── inactive.png │ │ │ └── pressed.png │ │ ├── go_cns │ │ │ ├── active.png │ │ │ ├── inactive.png │ │ │ └── pressed.png │ │ ├── go_new.png │ │ ├── go_synteny │ │ │ ├── active.png │ │ │ ├── inactive.png │ │ │ └── pressed.png │ │ ├── reload │ │ │ ├── active.png │ │ │ ├── inactive.png │ │ │ └── pressed.png │ │ ├── remove.png │ │ ├── remove │ │ │ ├── active.png │ │ │ ├── inactive.png │ │ │ └── pressed.png │ │ ├── remove_new.png │ │ └── sequence.png │ ├── minus.png │ └── plus.png ├── cancel.png ├── chromosome-small.png ├── chromosome2-small.png ├── colorpicker-images │ ├── Thumbs.db │ ├── blank.gif │ ├── colorpicker_background.png │ ├── colorpicker_hex.png │ ├── colorpicker_hsb_b.png │ ├── colorpicker_hsb_h.png │ ├── colorpicker_hsb_s.png │ ├── colorpicker_indic.gif │ ├── colorpicker_overlay.png │ ├── colorpicker_rgb_b.png │ ├── colorpicker_rgb_g.png │ ├── colorpicker_rgb_r.png │ ├── colorpicker_select.gif │ ├── colorpicker_submit.png │ ├── custom_background.png │ ├── custom_hex.png │ ├── custom_hsb_b.png │ ├── custom_hsb_h.png │ ├── custom_hsb_s.png │ ├── custom_indic.gif │ ├── custom_rgb_b.png │ ├── custom_rgb_g.png │ ├── custom_rgb_r.png │ ├── custom_submit.png │ ├── select.png │ ├── select2.png │ └── slider.png ├── comment-icon.png ├── default_user_image.png ├── delete.png ├── disc.png ├── disk.png ├── dna-icon-small.png ├── dna-icon.png ├── dna.png ├── error.png ├── feature-icon.png ├── gevo-synteny.png ├── gnome.jpg ├── group-icon-small.png ├── group-icon.png ├── home_page │ ├── 500px-3440_3441.CDS-CDS.blastn.dag_geneorder_D20_g10_A5.1-1.w800.png │ ├── 500px-Reconstructingchromosomes.png │ ├── 500px-SynPlot-Chr1-At-v-Al.png │ ├── 600px-CoGeBlast-At1g02120-eval.png │ ├── 600px-Maize-sorghum-cns.png │ ├── 600px-Phylogeny_fr_PhyML.png │ ├── 600px-Plasmodium-codon-substitution-matirx.png │ ├── 600px-SynPlot-Chr1-At-v-Al.png │ ├── 600px-Syntenic_dotplot_medicago_truncatula_v2_vs_v3.png │ ├── 600px-System_framework.png │ ├── 800px-GeLo-nucleotides.png │ ├── 800px-GenomeView_GEvo-links.png │ ├── 800px-Human-mouse-tandem-gene-duplication.png │ ├── 800px-Maize-sorghum-cns.png │ ├── 800px-Master_3068_8.CDS-CDS.blastn_geneorder_D20_g10_A5.w2000.ks.png │ ├── FeatMap-screenshot.png │ ├── GEvo-ecoli-insertion-direct-repeats.png │ ├── GenomeView-MG1655.png │ ├── Grapevine-peach_K2_historgram.png │ ├── Master_2361_2360.CDS-CDS.blastn_geneorder_D20_g10_A5.w500.png │ ├── Master_3068_8.CDS-CDS.blastn_geneorder_D20_g10_A5.w2000.ks.hist-1.png │ ├── OrganismView-search.png │ ├── Os-Sb-CNS-rich.png │ ├── Plasmodium_knowlesi_cds_gc_content_histogram.png │ ├── Three_minute_load_video.png │ ├── gevo-synteny.png │ ├── jbrowse-genome-view.png │ └── k12-CDS-aa-usage.png ├── in.png ├── jquery-ui-images │ ├── ui-bg_diagonals-small_100_f0efea_40x40.png │ ├── ui-bg_diagonals-small_95_ffe5ad_40x40.png │ ├── ui-bg_flat_35_f0f0f0_40x100.png │ ├── ui-bg_glow-ball_25_2e2e28_600x600.png │ ├── ui-bg_highlight-soft_100_e3eacc_1x100.png │ ├── ui-bg_highlight-soft_25_327E04_1x100.png │ ├── ui-bg_highlight-soft_25_5fac16_1x100.png │ ├── ui-bg_highlight-soft_55_edfcba_1x100.png │ ├── ui-bg_inset-soft_22_928868_1x100.png │ ├── ui-icons_67af2c_256x240.png │ ├── ui-icons_808080_256x240.png │ ├── ui-icons_8DC262_256x240.png │ ├── ui-icons_cd0a0a_256x240.png │ ├── ui-icons_ebebea_256x240.png │ ├── ui-icons_eeeeee_256x240.png │ └── ui-icons_ffffff_256x240.png ├── no-comment-icon.png ├── notebook-icon-small.png ├── notebook-icon.png ├── nsf-logo.gif ├── other │ ├── CoGe-icon.png │ ├── NCBI-icon.png │ ├── google-icon.png │ └── wikipedia-icon.png ├── out.png ├── page_not_found.png ├── preview │ ├── Blast.png │ ├── FeatView.png │ ├── GEvo.png │ ├── GeLo.png │ ├── GenomeView.png │ ├── MSAView.png │ ├── SynMap.png │ ├── TreeView.png │ └── app_schema.png ├── refresh-icon.png ├── server_error.png ├── smiley_default.png ├── smiley_default2.png ├── smiley_face.png ├── smileyface-icon.png ├── star-full.png ├── star-hollow.png ├── success.png ├── table │ ├── coge_table_bkgd_bottom.png │ ├── coge_table_bkgd_left.png │ ├── coge_table_bkgd_right.png │ ├── coge_table_bkgd_top.png │ ├── spacer-1x1.png │ ├── table_bg_body_b.png │ ├── table_bg_body_bl.png │ ├── table_bg_body_br.png │ ├── table_bg_body_l.png │ ├── table_bg_body_r.png │ ├── table_bg_body_t.png │ ├── table_bg_body_tl.png │ ├── table_bg_body_tr.png │ ├── table_bg_head_b.png │ ├── table_bg_head_bl.png │ ├── table_bg_head_br.png │ ├── table_bg_head_l.png │ ├── table_bg_head_r.png │ ├── table_bg_head_t.png │ ├── table_bg_head_tl.png │ └── table_bg_head_tr.png ├── tablesorter-pager-icons │ ├── first.png │ ├── last.png │ ├── next.png │ └── prev.png ├── tabs │ ├── loading.gif │ └── tab.png ├── test_tube.png ├── testtube-icon-small.png ├── testtube-icon.png ├── thumbs_down.png ├── thumbs_up.png ├── uc_seal.gif ├── urlicon │ └── favicon.ico ├── usda_logo.png ├── user-icon-small.png ├── user-icon.png ├── vr_icon.png ├── warning.png └── youtube-play-button.png ├── robots.txt ├── run_dotplot.pl ├── services ├── api.pl └── jex.py ├── setup.sh └── tRNAView.pl /.bowerrc: -------------------------------------------------------------------------------- 1 | { 2 | "directory": "web/js/vendor" 3 | } 4 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LyonsLab/coge/HEAD/.gitignore -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LyonsLab/coge/HEAD/.gitmodules -------------------------------------------------------------------------------- /.perltidyrc: -------------------------------------------------------------------------------- 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